NPASS Compound

Structure

NPC300419 OpenBabel07101719142D 66 73 0 0 1 0 0 0 0 0999 V2000 -9.4200 0.6637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0562 4.3070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0697 4.3070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7086 0.9865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8543 -1.4797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8543 -0.4932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0562 -2.3341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8543 1.4797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8543 -1.4797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4173 2.9595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7086 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4173 1.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5630 0.4932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7086 2.9595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5630 0.4932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0979 -2.2633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0704 0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7224 1.3612 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8543 1.4797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7086 1.9730 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4173 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.0233 0.4768 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3532 -1.3105 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8543 0.4932 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7086 -0.9865 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -12.2786 1.4296 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3060 -1.0552 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5614 -0.1023 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.2802 3.0117 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.5811 2.1272 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.3273 2.7563 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.9778 2.3141 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.8638 0.5953 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4173 -0.9865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.6282 1.8719 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0720 1.8035 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9109 0.3399 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0697 -2.3341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2605 0.7822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5630 3.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7086 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8543 0.4932 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5630 -1.4797 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5630 1.4797 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7954 -2.9609 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2716 0.4932 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.7208 -0.2208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.2315 1.6850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0036 -1.7527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5142 0.1530 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5355 3.9645 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.8364 3.0801 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6298 3.4539 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2716 -1.4797 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0832 -2.3341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5630 -3.1884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0052 -0.1707 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3729 0.9190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7696 1.1059 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6556 -0.6129 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.9306 2.5694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1191 1.5481 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2134 1.0375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 42 1 0 0 0 0 3 42 1 0 0 0 0 5 44 1 0 0 0 0 8 9 1 0 0 0 0 8 21 2 0 0 0 0 9 26 1 0 0 0 0 10 11 1 0 0 0 0 10 27 1 0 0 0 0 11 45 1 0 0 0 0 12 14 1 0 0 0 0 12 42 1 0 0 0 0 13 15 1 0 0 0 0 13 44 1 0 0 0 0 14 47 1 0 0 0 0 15 47 1 0 0 0 0 16 22 1 0 0 0 0 16 42 1 0 0 0 0 17 23 1 0 0 0 0 17 43 1 0 0 0 0 18 48 1 0 0 0 0 19 24 1 0 0 0 0 19 61 1 0 0 0 0 20 1 1 1 0 0 0 20 34 1 0 0 0 0 20 62 1 0 0 0 0 21 22 1 0 0 0 0 21 44 1 0 0 0 0 22 47 1 1 0 0 0 23 36 1 0 0 0 0 23 49 1 6 0 0 0 24 28 1 0 0 0 0 24 50 1 1 0 0 0 25 18 1 6 0 0 0 25 29 1 0 0 0 0 25 63 1 0 0 0 0 26 43 1 6 0 0 0 26 45 1 0 0 0 0 27 43 1 6 0 0 0 27 46 1 0 0 0 0 28 32 1 0 0 0 0 28 51 1 6 0 0 0 29 30 1 0 0 0 0 29 52 1 1 0 0 0 30 35 1 0 0 0 0 30 53 1 6 0 0 0 31 33 1 0 0 0 0 31 34 1 0 0 0 0 31 54 1 1 0 0 0 32 37 1 0 0 0 0 32 55 1 1 0 0 0 33 38 1 0 0 0 0 33 56 1 1 0 0 0 34 64 1 6 0 0 0 35 39 1 0 0 0 0 35 65 1 1 0 0 0 36 46 1 6 0 0 0 36 57 1 0 0 0 0 37 61 1 0 0 0 0 37 64 1 6 0 0 0 38 62 1 0 0 0 0 38 65 1 6 0 0 0 39 63 1 0 0 0 0 39 66 1 6 0 0 0 40 46 1 0 0 0 0 40 58 2 0 0 0 0 40 59 1 0 0 0 0 41 60 2 0 0 0 0 41 66 1 0 0 0 0 43 4 1 6 0 0 0 44 45 1 6 0 0 0 45 6 1 6 0 0 0 46 7 1 6 0 0 0 47 41 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	942.48
Volume:	912.121
LogP:	1.636
LogD:	1.471
LogS:	-3.473
# Rotatable Bonds:	9
TPSA:	312.05
# H-Bond Aceptor:	19
# H-Bond Donor:	11
# Rings:	8
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.111
Synthetic Accessibility Score:	6.426
Fsp3:	0.915
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.252
MDCK Permeability:	7.431559060933068e-05
Pgp-inhibitor:	0.314
Pgp-substrate:	0.992
Human Intestinal Absorption (HIA):	0.985
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.174
Plasma Protein Binding (PPB):	67.843505859375%
Volume Distribution (VD):	0.401
Pgp-substrate:	14.377262115478516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.817
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.255
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.045
CYP3A4-inhibitor:	0.075
CYP3A4-substrate:	0.011

ADMET: Excretion

Clearance (CL):	0.593
Half-life (T1/2):	0.641

ADMET: Toxicity

hERG Blockers:	0.095
Human Hepatotoxicity (H-HT):	0.211
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.092
Rat Oral Acute Toxicity:	0.096
Maximum Recommended Daily Dose:	0.046
Skin Sensitization:	0.023
Carcinogencity:	0.053
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.87

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC300419

Natural Product ID:	NPC300419
*Common Name:**	Polygalasaponin E
IUPAC Name:	(2S,3R,4S,4aR,6aR,6bS,8aS,12aS,14aR,14bR)-8a-[(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5R,6S)-3,4-dihydroxy-6-methyl-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxycarbonyl-2,3-dihydroxy-4,6a,6b,11,11,14b-hexamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicene-4-carboxylic acid
Synonyms:	polygalasaponin E
Standard InCHIKey:	AWUKSVPVFAMJKF-UCOQPZAKSA-N
Standard InCHI:	InChI=1S/C47H74O19/c1-20-34(64-37-32(55)28(51)24(50)19-61-37)31(54)33(56)38(62-20)65-35-30(53)29(52)25(18-48)63-39(35)66-41(60)47-14-12-42(2,3)16-22(47)21-8-9-26-43(4)17-23(49)36(57)46(7,40(58)59)27(43)10-11-45(26,6)44(21,5)13-15-47/h8,20,22-39,48-57H,9-19H2,1-7H3,(H,58,59)/t20-,22-,23-,24+,25+,26+,27+,28-,29+,30-,31-,32+,33+,34-,35+,36-,37-,38-,39-,43+,44+,45+,46-,47-/m0/s1
SMILES:	OC[C@H]1O[C@@H](OC(=O)[C@]23CC[C@@]4(C(=CC[C@H]5[C@@]4(C)CC[C@@H]4[C@]5(C)C[C@@H]([C@@H]([C@@]4(C)C(=O)O)O)O)[C@@H]3CC(CC2)(C)C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O[C@@H]1OC[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL503227
PubChem CID:	11571566
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643032]
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Others	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	35.4	%	PMID[532797]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	58.1	%	PMID[532797]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC300419 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	273
0.1-0.2	1828
0.2-0.3	5176
0.3-0.4	11045
0.4-0.5	10960
0.5-0.6	6521
0.6-0.7	3891
0.7-0.8	1859
0.8-0.85	463
0.85-0.9	260
0.9-0.95	205
0.95-1	216

Similarity Score	Similarity Level	Natural Product ID
0.9907	High Similarity	NPC291903
0.9907	High Similarity	NPC37134
0.9815	High Similarity	NPC475119
0.9815	High Similarity	NPC473824
0.9813	High Similarity	NPC475486
0.9813	High Similarity	NPC164389
0.9727	High Similarity	NPC473645
0.9725	High Similarity	NPC232237
0.9725	High Similarity	NPC105800
0.9725	High Similarity	NPC237191
0.9722	High Similarity	NPC305267
0.9722	High Similarity	NPC26626
0.9722	High Similarity	NPC51465
0.9722	High Similarity	NPC75287
0.9722	High Similarity	NPC476992
0.9722	High Similarity	NPC288205
0.972	High Similarity	NPC96641
0.972	High Similarity	NPC473343
0.972	High Similarity	NPC163183
0.972	High Similarity	NPC150400
0.972	High Similarity	NPC134835
0.972	High Similarity	NPC73318
0.972	High Similarity	NPC475208
0.972	High Similarity	NPC238935
0.9636	High Similarity	NPC471577
0.9636	High Similarity	NPC207738
0.9633	High Similarity	NPC309223
0.9633	High Similarity	NPC102505
0.9633	High Similarity	NPC33012
0.9633	High Similarity	NPC475209
0.9633	High Similarity	NPC191827
0.9633	High Similarity	NPC470876
0.9633	High Similarity	NPC85154
0.9633	High Similarity	NPC104137
0.9633	High Similarity	NPC69811
0.9633	High Similarity	NPC220160
0.9633	High Similarity	NPC323359
0.9633	High Similarity	NPC123522
0.9633	High Similarity	NPC473452
0.9633	High Similarity	NPC8524
0.9633	High Similarity	NPC475514
0.9633	High Similarity	NPC286457
0.9626	High Similarity	NPC104400
0.9626	High Similarity	NPC471383
0.9626	High Similarity	NPC104071
0.9626	High Similarity	NPC324875
0.9626	High Similarity	NPC276093
0.9626	High Similarity	NPC109079
0.9626	High Similarity	NPC48249
0.9626	High Similarity	NPC79718
0.9626	High Similarity	NPC473383
0.9626	High Similarity	NPC475504
0.9626	High Similarity	NPC292677
0.9626	High Similarity	NPC101744
0.9626	High Similarity	NPC473373
0.9626	High Similarity	NPC80843
0.9626	High Similarity	NPC1046
0.9626	High Similarity	NPC10320
0.9626	High Similarity	NPC139044
0.9626	High Similarity	NPC257468
0.9626	High Similarity	NPC469946
0.9626	High Similarity	NPC102439
0.9626	High Similarity	NPC139894
0.9626	High Similarity	NPC475516
0.9554	High Similarity	NPC213952
0.955	High Similarity	NPC142151
0.955	High Similarity	NPC267694
0.955	High Similarity	NPC110385
0.955	High Similarity	NPC144644
0.955	High Similarity	NPC37860
0.955	High Similarity	NPC153673
0.9545	High Similarity	NPC470514
0.9545	High Similarity	NPC473459
0.9545	High Similarity	NPC470513
0.9541	High Similarity	NPC58448
0.9541	High Similarity	NPC160415
0.9541	High Similarity	NPC471384
0.9541	High Similarity	NPC161674
0.9537	High Similarity	NPC309714
0.9537	High Similarity	NPC46665
0.9537	High Similarity	NPC114304
0.9537	High Similarity	NPC251263
0.9537	High Similarity	NPC475287
0.9537	High Similarity	NPC475467
0.9537	High Similarity	NPC258885
0.9537	High Similarity	NPC133818
0.9537	High Similarity	NPC114287
0.9537	High Similarity	NPC151543
0.9537	High Similarity	NPC219180
0.9537	High Similarity	NPC192600
0.9537	High Similarity	NPC323341
0.9537	High Similarity	NPC155410
0.9537	High Similarity	NPC124296
0.9537	High Similarity	NPC166422
0.9537	High Similarity	NPC174720
0.9537	High Similarity	NPC241909
0.9537	High Similarity	NPC295823
0.9537	High Similarity	NPC473826
0.9533	High Similarity	NPC31839
0.9533	High Similarity	NPC179434
0.9533	High Similarity	NPC164419
0.9469	High Similarity	NPC257211
0.9464	High Similarity	NPC62725
0.9464	High Similarity	NPC68767
0.9464	High Similarity	NPC297263
0.9464	High Similarity	NPC11242
0.9464	High Similarity	NPC223301
0.9464	High Similarity	NPC114484
0.9464	High Similarity	NPC301449
0.9464	High Similarity	NPC31838
0.9464	High Similarity	NPC22956
0.9464	High Similarity	NPC293031
0.9464	High Similarity	NPC159309
0.9464	High Similarity	NPC64715
0.9464	High Similarity	NPC222580
0.9464	High Similarity	NPC86222
0.9464	High Similarity	NPC171544
0.9464	High Similarity	NPC104372
0.9464	High Similarity	NPC51099
0.9464	High Similarity	NPC275225
0.9459	High Similarity	NPC135849
0.9459	High Similarity	NPC25663
0.9459	High Similarity	NPC473386
0.9459	High Similarity	NPC51564
0.9455	High Similarity	NPC471580
0.9455	High Similarity	NPC68175
0.9455	High Similarity	NPC148417
0.9455	High Similarity	NPC110633
0.9455	High Similarity	NPC136768
0.9455	High Similarity	NPC471547
0.945	High Similarity	NPC476068
0.945	High Similarity	NPC204414
0.945	High Similarity	NPC469782
0.945	High Similarity	NPC161717
0.945	High Similarity	NPC70809
0.945	High Similarity	NPC250247
0.945	High Similarity	NPC471385
0.945	High Similarity	NPC57484
0.945	High Similarity	NPC60557
0.945	High Similarity	NPC294453
0.945	High Similarity	NPC224381
0.945	High Similarity	NPC227551
0.945	High Similarity	NPC54636
0.945	High Similarity	NPC471550
0.945	High Similarity	NPC100639
0.945	High Similarity	NPC309907
0.945	High Similarity	NPC305981
0.945	High Similarity	NPC298034
0.945	High Similarity	NPC65105
0.945	High Similarity	NPC473714
0.945	High Similarity	NPC79643
0.945	High Similarity	NPC119592
0.945	High Similarity	NPC475160
0.945	High Similarity	NPC236638
0.945	High Similarity	NPC76972
0.945	High Similarity	NPC67857
0.945	High Similarity	NPC123199
0.945	High Similarity	NPC261506
0.945	High Similarity	NPC43550
0.945	High Similarity	NPC202828
0.945	High Similarity	NPC293330
0.945	High Similarity	NPC71065
0.945	High Similarity	NPC4328
0.945	High Similarity	NPC475140
0.945	High Similarity	NPC41061
0.9444	High Similarity	NPC256798
0.9444	High Similarity	NPC116794
0.9444	High Similarity	NPC128925
0.9439	High Similarity	NPC136877
0.9439	High Similarity	NPC56713
0.9439	High Similarity	NPC68419
0.9439	High Similarity	NPC475296
0.9439	High Similarity	NPC7870
0.9439	High Similarity	NPC59804
0.9439	High Similarity	NPC90856
0.9439	High Similarity	NPC174679
0.9439	High Similarity	NPC108709
0.9439	High Similarity	NPC279554
0.9439	High Similarity	NPC242611
0.9439	High Similarity	NPC270667
0.9439	High Similarity	NPC199457
0.9439	High Similarity	NPC164194
0.9439	High Similarity	NPC474589
0.9439	High Similarity	NPC102914
0.9439	High Similarity	NPC29069
0.9439	High Similarity	NPC75747
0.9439	High Similarity	NPC110139
0.9439	High Similarity	NPC127056
0.9386	High Similarity	NPC33068
0.9381	High Similarity	NPC162574
0.9381	High Similarity	NPC475591
0.9381	High Similarity	NPC4749
0.9381	High Similarity	NPC21691
0.9381	High Similarity	NPC80986
0.9381	High Similarity	NPC187290
0.9381	High Similarity	NPC10607
0.9381	High Similarity	NPC236870
0.9375	High Similarity	NPC476991
0.9375	High Similarity	NPC118440
0.9375	High Similarity	NPC236657

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC300419 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	256
0.1-0.2	2170
0.2-0.3	3815
0.3-0.4	1902
0.4-0.5	584
0.5-0.6	285
0.6-0.7	105
0.7-0.8	29
0.8-0.85	1
0.85-0.9	1
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.913	High Similarity	NPD8328	Phase 3
0.8938	High Similarity	NPD8295	Clinical (unspecified phase)
0.8818	High Similarity	NPD8132	Clinical (unspecified phase)
0.8348	Intermediate Similarity	NPD8133	Approved
0.7869	Intermediate Similarity	NPD8513	Phase 3
0.7869	Intermediate Similarity	NPD8516	Approved
0.7869	Intermediate Similarity	NPD8515	Approved
0.7869	Intermediate Similarity	NPD8517	Approved
0.7826	Intermediate Similarity	NPD6412	Phase 2
0.7787	Intermediate Similarity	NPD8294	Approved
0.7787	Intermediate Similarity	NPD8377	Approved
0.7759	Intermediate Similarity	NPD6686	Approved
0.7748	Intermediate Similarity	NPD7902	Approved
0.7724	Intermediate Similarity	NPD8378	Approved
0.7724	Intermediate Similarity	NPD8296	Approved
0.7724	Intermediate Similarity	NPD8379	Approved
0.7724	Intermediate Similarity	NPD8380	Approved
0.7724	Intermediate Similarity	NPD8335	Approved
0.7717	Intermediate Similarity	NPD7319	Approved
0.7638	Intermediate Similarity	NPD7736	Approved
0.7636	Intermediate Similarity	NPD7748	Approved
0.7619	Intermediate Similarity	NPD7507	Approved
0.7581	Intermediate Similarity	NPD8033	Approved
0.7477	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.7477	Intermediate Similarity	NPD7900	Approved
0.7455	Intermediate Similarity	NPD7515	Phase 2
0.7422	Intermediate Similarity	NPD8293	Discontinued
0.7419	Intermediate Similarity	NPD7516	Approved
0.7339	Intermediate Similarity	NPD7327	Approved
0.7339	Intermediate Similarity	NPD7328	Approved
0.7311	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.7244	Intermediate Similarity	NPD6370	Approved
0.7203	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7165	Intermediate Similarity	NPD7503	Approved
0.7143	Intermediate Similarity	NPD8034	Phase 2
0.7143	Intermediate Similarity	NPD8035	Phase 2
0.7132	Intermediate Similarity	NPD7492	Approved
0.7131	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7087	Intermediate Similarity	NPD6059	Approved
0.7087	Intermediate Similarity	NPD6054	Approved
0.7087	Intermediate Similarity	NPD6319	Approved
0.7077	Intermediate Similarity	NPD6616	Approved
0.7023	Intermediate Similarity	NPD7078	Approved
0.6984	Remote Similarity	NPD7115	Discovery
0.6967	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD8297	Approved
0.6935	Remote Similarity	NPD6882	Approved
0.693	Remote Similarity	NPD6399	Phase 3
0.6923	Remote Similarity	NPD7638	Approved
0.6911	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6899	Remote Similarity	NPD6016	Approved
0.6899	Remote Similarity	NPD6015	Approved
0.6894	Remote Similarity	NPD8074	Phase 3
0.6864	Remote Similarity	NPD7639	Approved
0.6864	Remote Similarity	NPD7640	Approved
0.685	Remote Similarity	NPD6009	Approved
0.6846	Remote Similarity	NPD5988	Approved
0.6842	Remote Similarity	NPD6411	Approved
0.6829	Remote Similarity	NPD6373	Approved
0.6829	Remote Similarity	NPD6372	Approved
0.6822	Remote Similarity	NPD7645	Phase 2
0.6794	Remote Similarity	NPD6067	Discontinued
0.6783	Remote Similarity	NPD8171	Discontinued
0.678	Remote Similarity	NPD4225	Approved
0.6769	Remote Similarity	NPD6921	Approved
0.6757	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6746	Remote Similarity	NPD4632	Approved
0.6721	Remote Similarity	NPD6402	Approved
0.6721	Remote Similarity	NPD5739	Approved
0.6721	Remote Similarity	NPD7128	Approved
0.6721	Remote Similarity	NPD6675	Approved
0.672	Remote Similarity	NPD6650	Approved
0.672	Remote Similarity	NPD6649	Approved
0.6667	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6101	Approved
0.6667	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6613	Remote Similarity	NPD7320	Approved
0.6613	Remote Similarity	NPD6881	Approved
0.6613	Remote Similarity	NPD6899	Approved
0.6593	Remote Similarity	NPD6033	Approved
0.6587	Remote Similarity	NPD8130	Phase 1
0.6552	Remote Similarity	NPD7983	Approved
0.6549	Remote Similarity	NPD3618	Phase 1
0.6532	Remote Similarity	NPD5697	Approved
0.6532	Remote Similarity	NPD5701	Approved
0.6508	Remote Similarity	NPD7290	Approved
0.6508	Remote Similarity	NPD4634	Approved
0.6508	Remote Similarity	NPD6883	Approved
0.6508	Remote Similarity	NPD7102	Approved
0.6496	Remote Similarity	NPD5779	Approved
0.6496	Remote Similarity	NPD5778	Approved
0.6475	Remote Similarity	NPD8450	Suspended
0.6466	Remote Similarity	NPD46	Approved
0.6466	Remote Similarity	NPD6698	Approved
0.6457	Remote Similarity	NPD6847	Approved
0.6457	Remote Similarity	NPD6869	Approved
0.6457	Remote Similarity	NPD6617	Approved
0.6452	Remote Similarity	NPD6008	Approved
0.6435	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD6012	Approved
0.6429	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD3669	Approved
0.6429	Remote Similarity	NPD6014	Approved
0.6429	Remote Similarity	NPD6013	Approved
0.6418	Remote Similarity	NPD7604	Phase 2
0.6417	Remote Similarity	NPD6084	Phase 2
0.6417	Remote Similarity	NPD6083	Phase 2
0.6403	Remote Similarity	NPD8449	Approved
0.6397	Remote Similarity	NPD8448	Approved
0.6391	Remote Similarity	NPD5983	Phase 2
0.6379	Remote Similarity	NPD5328	Approved
0.6377	Remote Similarity	NPD8390	Approved
0.6377	Remote Similarity	NPD8392	Approved
0.6377	Remote Similarity	NPD8391	Approved
0.6372	Remote Similarity	NPD4786	Approved
0.637	Remote Similarity	NPD8340	Approved
0.637	Remote Similarity	NPD8299	Approved
0.637	Remote Similarity	NPD8341	Approved
0.637	Remote Similarity	NPD8342	Approved
0.6364	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.635	Remote Similarity	NPD8337	Approved
0.635	Remote Similarity	NPD8336	Approved
0.6349	Remote Similarity	NPD6011	Approved
0.6348	Remote Similarity	NPD3573	Approved
0.6341	Remote Similarity	NPD7632	Discontinued
0.6339	Remote Similarity	NPD3667	Approved
0.6336	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6328	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6324	Remote Similarity	NPD8451	Approved
0.6324	Remote Similarity	NPD6336	Discontinued
0.6286	Remote Similarity	NPD8338	Approved
0.6284	Remote Similarity	NPD7625	Phase 1
0.6281	Remote Similarity	NPD4755	Approved
0.6271	Remote Similarity	NPD6079	Approved
0.6261	Remote Similarity	NPD7146	Approved
0.6261	Remote Similarity	NPD5330	Approved
0.6261	Remote Similarity	NPD7521	Approved
0.6261	Remote Similarity	NPD7334	Approved
0.6261	Remote Similarity	NPD6684	Approved
0.6261	Remote Similarity	NPD6409	Approved
0.626	Remote Similarity	NPD6940	Discontinued
0.625	Remote Similarity	NPD1780	Approved
0.625	Remote Similarity	NPD1779	Approved
0.6239	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.623	Remote Similarity	NPD5696	Approved
0.6218	Remote Similarity	NPD4202	Approved
0.6198	Remote Similarity	NPD7839	Suspended
0.6198	Remote Similarity	NPD4697	Phase 3
0.6179	Remote Similarity	NPD4700	Approved
0.6179	Remote Similarity	NPD5286	Approved
0.6179	Remote Similarity	NPD4696	Approved
0.6179	Remote Similarity	NPD5285	Approved
0.6176	Remote Similarity	NPD7830	Approved
0.6176	Remote Similarity	NPD7829	Approved
0.6161	Remote Similarity	NPD7525	Registered
0.6154	Remote Similarity	NPD6903	Approved
0.6154	Remote Similarity	NPD8387	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD5737	Approved
0.6154	Remote Similarity	NPD6672	Approved
0.6148	Remote Similarity	NPD8444	Approved
0.6148	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6143	Remote Similarity	NPD5956	Approved
0.6142	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6136	Remote Similarity	NPD6274	Approved
0.6134	Remote Similarity	NPD7637	Suspended
0.6129	Remote Similarity	NPD5344	Discontinued
0.6126	Remote Similarity	NPD6118	Approved
0.6126	Remote Similarity	NPD6115	Approved
0.6126	Remote Similarity	NPD6697	Approved
0.6126	Remote Similarity	NPD6114	Approved
0.6124	Remote Similarity	NPD6371	Approved
0.6121	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6119	Remote Similarity	NPD7101	Approved
0.6119	Remote Similarity	NPD7100	Approved
0.6116	Remote Similarity	NPD5695	Phase 3
0.6116	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6103	Remote Similarity	NPD8080	Discontinued
0.6087	Remote Similarity	NPD3666	Approved
0.6087	Remote Similarity	NPD3133	Approved
0.6087	Remote Similarity	NPD3665	Phase 1
0.6084	Remote Similarity	NPD8415	Approved
0.608	Remote Similarity	NPD5224	Approved
0.608	Remote Similarity	NPD5225	Approved
0.608	Remote Similarity	NPD5226	Approved
0.608	Remote Similarity	NPD4633	Approved
0.608	Remote Similarity	NPD5211	Phase 2
0.6066	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.6066	Remote Similarity	NPD5222	Approved
0.6066	Remote Similarity	NPD5221	Approved
0.6063	Remote Similarity	NPD4767	Approved
0.6063	Remote Similarity	NPD4768	Approved
0.6045	Remote Similarity	NPD7641	Discontinued
0.6045	Remote Similarity	NPD6335	Approved
0.6036	Remote Similarity	NPD6116	Phase 1
0.6033	Remote Similarity	NPD5282	Discontinued
0.6032	Remote Similarity	NPD5175	Approved
0.6032	Remote Similarity	NPD5174	Approved
0.6029	Remote Similarity	NPD6908	Approved
0.6029	Remote Similarity	NPD6909	Approved
0.6016	Remote Similarity	NPD5173	Approved

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data